HIV-1 evolution in the female genital tract and trafficking to the blood

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DESCRIPTION (provided by applicant): In the mid-1990's, modeling of viral decay predicted that antiretroviral therapy (ART) would result in clearance of HIV infection with ~3 years of treatment. However, HIV was found to persist during suppressive ART. The half-life of infection was estimated to extend for many years, such that viral clearance would not be expected to occur during a normal life span. Our and others' studies of HIV that persists during suppressive ART have observed low-level viral replication in a minority (~20%) of individuals. We have studied HIV persisting in blood, sputum and genital tissues, all of which could serve as potential viral reservoirs during effective ART. Utilizing single genome amplification (SGA), we independently-derived and directly sequenced (to avoid detection of PCR-mediated mutations) sufficient viral templates from multiple specimens to characterize viral populations and their changes during suppressive ART. We detected sizable populations of identical viral genomes, here termed monotypic virus, in various cell types. SGA of low-level plasma viral blips (<500c/mL) revealed monotypic viruses in individuals that phylogenetic and drug resistance analyses showed no evidence of viral replication. We reason that blips of monotypic virus could result from production of virions without full- cycles of replication, as nucleoside- and non-nucleoside reverse transcriptase inhibitors (NRTI and NNRTI) would prevent infection of additional cells. As estimates of viral burst size suggest that a single HIV infected cell could not produce sufficient virions to generate a viral load of 50-500c/mL, this gave further support to a developing hypothesis that HIV proviruses are amplified in proliferating cells, and that at times these cells produce virions without full rounds of infection. If our hypothesis is correct, cellular proliferation could be an important mechanism that over time perpetuates HIV infection, a concept that has not been previously characterized. The hypotheses of this proposal are that: (1) Clonal expansion (i.e., proliferation) of HIV infected cells results in multiple cells, each with an identical viral sequence integrated at the same site in the host's genome. (2) A substantial proportion of viruses detected in the female genital mucosa and blood are derived from the proliferation of HIV infected cells, and these viruses become more prominent during suppressive ART. (3) Monotypic proviral sequences include templates that are replication competent. We Aim to: 1: Determine if monotypic (identical) HIV env sequences in the uterine cervix result from proliferation of infected cells or from bursts of viral replication 2: Determine if whole monotypic HIV genomes include replication competent viruses Our proposed studies exploring the role of cellular proliferation in perpetuating HIV infection could alter current paradigms explaining viral persistence and shape interventions needed to cure HIV.